In this paper, we present a case study on freight railway transportation in Italy, which is a by-product of research collaboration with a major Italian railway company. We highlight the main features of the Italian reality and propose a customized mathematical model to design the service network, that is, the set of origin-destination connections. More specifically, the model suggests the services to provide, the number of trains travelling on each connection, the number of cars and their type. We consider both full and empty freight car movements and take handling costs into account. All decisions are taken in order to minimize the total costs. The quality of service is guaranteed by satisfying all the transportation demand and by implicitly minimizing the waiting time of cars at intermediate railway stations. Our approach yields to a multi-commodity network design problem with a concave cost function. To solve this problem, we implement a specialized tabu search procedure. Computational results on realistic instances show a significant improvement over current practice.